miRNA: 3'- aUGUGCCUGC-UAGUCga-GCGGA--GGCa -5'
miRNA: 3'- -AUGUGCCUGC-------------UAG--------------UCGAGCGG--AGGCA- -5'
miRNA: 3'- aUGUGCCUGCUaG---------------UCGAGCGG---AGGCA- -5'
miRNA: 3'- -AUGUGCCUGCUAGUCGAGCGGAGGCA- -5'
Results 1 - 4 of 4 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position | R_P_ratio# |
P value
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| Predicted miRNA align pattern | |||||||
| 30621 | 3' | -57.2 | NC_006549.1 | + | 73261 | 0.68 | 0.748433 |
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Target: 5'- aACACGGGCGcAUCAGacaCGCCUuuUCGg -3' miRNA: 3'- aUGUGCCUGC-UAGUCga-GCGGA--GGCa -5' |
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| 30621 | 3' | -57.2 | NC_006549.1 | + | 52666 | 0.7 | 0.603065 |
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Target: 5'- aUACGCGGACGcggaggaggauugGUCcgcgugggccagggAGCUCGCCgaUCCGUc -3' miRNA: 3'- -AUGUGCCUGC-------------UAG--------------UCGAGCGG--AGGCA- -5' |
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| 30621 | 3' | -57.2 | NC_006549.1 | + | 3955 | 0.75 | 0.351489 |
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Target: 5'- gACACGGACGAaCccuuuuuguggcccgAGCUCGCCuacUCCGUa -3' miRNA: 3'- aUGUGCCUGCUaG---------------UCGAGCGG---AGGCA- -5' |
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| 30621 | 3' | -57.2 | NC_006549.1 | + | 130300 | 1.06 | 0.003087 |
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Target: 5'- gUACACGGACGAUCAGCUCGCCUCCGUg -3' miRNA: 3'- -AUGUGCCUGCUAGUCGAGCGGAGGCA- -5' |
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Note:
When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.
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